Biology subjects

Han, D.

Publications and source records attributed to Han, D..

At least 73 records · Page 4Linked to original sources

bioRxiv2021

Outcomes of Progranulin Gene Therapy in the Retina are Dependent on Time of Delivery

Neuronal ceroid lipofuscinosis (NCL) is a family of neurodegenerative diseases caused by mutations to genes related to lysosomal function. One variant, CNL11, is caused by mutations to the gene encoding the protein progranulin. Primarily secreted by microglia, progranulin regulates neuronal lysosomal function once endocytosed. Absence of progranulin causes cerebellar atrophy, seizures, ataxia, dementia and vision loss. As progranulin gene therapies targeting the brain are developed, it is also advantageous to focus on the retina, as its characteristics are beneficial for gene therapy development: the retina is easily visible through direct imaging, can be assessed through quantitative methods in vivo, requires smaller amounts of AAV and AAV can be administered via a less invasive surgery. In this study we characterize the retinal degeneration in a progranulin knockout mouse model of CLN11 and study the effects of gene replacement at different time points. All mice heterologously expressing progranulin showed reduction in lipofuscin deposits and microglia infiltration. While mice that receive systemic AAV9.2YF-scCAG-PGRN at post-natal day 3 or 4 show a reduction in retina thinning, mice injected intravitreally at months 1 and 6 with 7m8-scCAG-PGRN show no improvement, and mice injected at 12 months of age show increased retinal thinning in comparison to their controls. Thus, delivery of progranulin proves to be time-sensitive, requiring early administration for optimal therapeutic benefit.

neuroscience↗

bioRxiv2021

Extracellular vesicles induce aggressive phenotype of luminal breast cancer cells by PKM2 phosphorylation

The aerobic glycolysis is a hallmark of cancer glucose metabolism. Several studies have suggested that cancer-derived extracellular vesicles (EVs) can modulate glucose metabolism in adjacent cells and promote disease progression. Here we suggest that EVs originated from cancer cell with highly glycolytic activity can modulate glucose metabolism in the recipient cancer cells with relative low glycolytic activity, and further induce cell proliferation. Two types of breast cancer cell lines with different levels of glycolytic activity, MDA-MB-231 of a claudin low-type breast cancer cell and MCF7 of luminal type breast cancer cell, were selected and co-cultured using indirect co-culture system such as transwell system or microfluidic system. Glucose uptake of the recipient MCF7 cells was markedly increased after co-culture with MDA-MB-231 cells. MCF7 cells after co-culture with MDA-MB-231-tdTomato cells represented multiple tdTomato signal inside the cell, which proved that EVs originated from MDA-MB-231-tdTomato were transferred to MCF7 cell. In addition, serine phosphorylation of PKM2 necessary for tumorigenesis was highly activated, and tyrosine phosphorylation of PKM2 suggesting activated aerobic glycolysis was also increased in the co-cultured MCF7 cells. Proteomic profiling of the co-cultured MCF7 cells revealed the proliferation and dedifferentiation of MCF7 cells, and further confirmed epithelial-mesenchymal transition (EMT), which is a key phenomenon for cancer metastasis. In the transcriptomic analysis, glycolysis increased in co-cultured MCF7 cells, and the component analysis of genes associated with glycolysis revealed that the next major component after cytoplasm was extracellular exosome. Proteomic analysis of EVs revealed that there were important proteins in the EV such as EGFR, ERBB2 and MAPK for phosphorylating PKM2. This phenomenon suggests the potential for aggressive cancer cells to affect other cancer cells through EV mediators.

cancer biology↗

bioRxiv2020

A novel high-accuracy genome assembly method utilizing a high-throughput workflow

Across domains of biological research using genome sequence data, high-quality reference genome sequences are essential for characterizing genetic variation and understanding the genetic basis of phenotypes. However, the construction of genome assemblies for various species is often hampered by complexities of genome organization, especially repetitive and complex sequences, leading to mis-assembly and missing regions. Here, we describe a high-throughput gold standard genome assembly workflow using a large-scale bacterial artificial chromosome (BAC) library with a refined two-step pooling strategy and the Lamp assembler algorithm. This strategy minimizes the laborious processes of physical map construction and clone-by-clone sequencing, enabling inexpensive sequencing of several thousand BAC clones. By applying this strategy with a minimum tiling path BAC clone library for the short arm of chromosome 2D (2DS) of bread wheat, 98% of BAC sequences, covering 92.7% of the 2DS chromosome, were assembled correctly for this species with a highly complex and repetitive genome. We also identified 48 large mis-assemblies in the reference wheat genome assembly (IWGSC RefSeq v1.0) and corrected these large mis-assemblies in addition to filling 92.2% of the gaps in RefSeq v1.0. Our 2DS assembly represents a new benchmark for the assembly of complex genomes with both high accuracy and efficiency.

genomics↗

bioRxiv2020

The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR

On 22 January 2020, the National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), created the 2019 Novel Coronavirus Resource (2019nCoVR), an open-access SARS-CoV-2 information resource. 2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates, which are manually curated with value-added annotations and quality evaluated by our in-house automated pipeline. Of particular note, 2019nCoVR performs systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale. It provides all identified variants and detailed statistics for each virus isolate, and congregates the quality score, functional annotation, and population frequency for each variant. It also generates visualization of the spatiotemporal change for each variant and yields historical viral haplotype network maps for the course of the outbreak from all complete and high-quality genomes. Moreover, 2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on COVID-19 (Coronavirus Disease 2019), including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC. Furthermore, by linking with relevant databases in CNCB-NGDC, 2019nCoVR offers data submission services for raw sequence reads and assembled genomes, and data sharing with National Center for Biotechnology Information. Collectively, all SARS-CoV-2 genome sequences, variants, haplotypes and literature are updated daily to provide timely information, making 2019nCoVR a valuable resource for the global research community. 2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.

genomics↗

bioRxiv2020

In-depth analysis reveals complex molecular etiology of idiopathic cerebral palsy

Cerebral palsy (CP), the most prevalent physical disability in children, has long been ignored with regard to its inherent molecular mechanism. In this work, we performed in-depth clinical and molecular analysis on 120 idiopathic CP families, and identified in half of the patients the underlying risk factors. By a compilation of 117 CP-related genes, we recognized the characteristic features in terms of inheritance and function, and proposed a dichotomous classification system according to the expression patterns. In two patients with both CP and intellectual disability, we revealed that the defective TYW1, a tRNA hypermodification enzyme, caused microcephaly and problems in motion and cognition by hindering neuronal proliferation and migration. We developed an algorithm and proved in mice brain that this malfunctioning hypermodification specifically perturbed the translation of a subset of proteins involved in cell cycling. In a CP patient with normal intelligence, we identified a mitochondrial enzyme GPAM, the hypomorphic form of which led to hypomyelination of corticospinal tract. We confirmed that the aberrant Gpam in mice perturbed the lipid metabolism in astrocyte, resulting in suppressed astrocyte proliferation and a shortage of lipid contents supplied for oligodendrocyte myelination. This work broadened the scope of understanding of CP etiology and paved a way for innovative therapeutic strategies.

genetics↗

bioRxiv2020

In-depth blood proteome profiling analysis revealed distinct functional characteristics of plasma proteins between severe and non-severe COVID-19 patients

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected over ten million patients worldwide. Although most coronavirus disease 2019 (COVID-19) patients have a good prognosis, some develop severe illness. Markers that define disease severity or predict clinical outcome need to be urgently developed as the mortality rate in critical cases is approximately 61.5%. In the present study, we performed indepth proteome profiling of undepleted plasma from eight COVID-19 patients. Quantitative proteomic analysis using the BoxCar method revealed that 91 out of 1,222 quantified proteins were differentially expressed depending on the severity of COVID-19. Importantly, we found 76 proteins, previously not reported, which could be novel prognostic biomarker candidates. Our plasma proteome signatures captured the host response to SARS-CoV-2 infection, thereby highlighting the role of neutrophil activation, complement activation, platelet function, and T cell suppression as well as proinflammatory factors upstream and downstream of interleukin-6, interleukin-1B, and tumor necrosis factor. Consequently, this study supports the development of blood biomarkers and potential therapeutic targets to aid clinical decision-making and subsequently improve prognosis of COVID-19.

systems biology↗

bioRxiv2020

A dynamic and spatially periodic micro-pattern of HES5 expression underlies the probability of neuronal differentiation in the mouse spinal cord

Ultradian oscillations of HES Transcription Factors (TFs) at the single cell level, enable cell state transitions. However, the tissue level organisation of HES5 dynamics in neurogenesis is unknown. Here, we analyse the expression of HES5 ex-vivo in the developing mouse ventral spinal cord and identify microclusters of 4-6 cells with positively correlated HES5 level and ultradian dynamics. These microclusters are spatially periodic along the dorsoventral axis and temporally dynamic, alternating between high and low expression with a supra-ultradian persistence time. We show that Notch signaling is required for temporal dynamics but not the spatial periodicity of HES5. Few Neurogenin-2 cells are observed per cluster, irrespective of high or low state, suggesting that the microcluster organization of HES5 enables the stable selection of differentiating cells. Computational modelling predicts that different cell coupling strengths underlie the HES5 spatial patterns and rate of differentiation, which is consistent with comparison between the motoneuron and interneuron progenitor domains. Our work shows a previously unrecognised spatiotemporal organisation of neurogenesis, emergent at the tissue level from the synthesis of single cell dynamics. SynopsisLive imaging of HES5 expression in the ventral mouse spinal cord together with computational modelling is used to identify and analyse spatially periodic HES5 micro-patterns that emerge from the synthesis of single cell dynamics. O_LIHES5 is expressed in spatially periodic microclusters along the dorsal-ventral axis in spinal cord that are dynamically maintained by Notch signalling. C_LIO_LIMicroclusters can arise, in part, from single cell oscillators that are synchronous and weakly coupled via Notch. C_LIO_LISpatial patterns are different between motorneuron and interneuron progenitor domains and the probability for progenitor differentiation is regulated by the coupling strength between cells. C_LIO_LINGN2 is also spatially periodic along the dorso-ventral axis and microclusters of HES5 may act to pick a single NGN2 high cell for differentiation. C_LI

developmental biology↗

bioRxiv2020

Unannotated small RNA clusters in circulating extracellular vesicles detect early stage liver cancer

BackgroundHepatocellular carcinoma (HCC) is among the deadliest malignancies and surveillance tools for early detection are suboptimal. Extracellular vesicles (EVs) have gained increasing scientific interest due to their involvement in tumor initiation and metastasis, however, most extracellular RNA (exRNA) biomarker studies are limited to annotated genomic regions. MethodsEVs were isolated with ultracentrifugation and nanoDLD and quality assessed by electron microscopy, immunoblotting, nanoparticle tracking, and deconvolution analysis. We performed genome-wide small exRNA sequencing, including unannotated transcripts. We identified small RNA clusters (smRCs) and delineated their key genomic features across biospecimens (blood, urine, tissue) and EV isolation techniques. A 3-smRC signature for early HCC detection was trained and validated in two independent cohorts. ResultsEV-derived smRCs were dominated by uncharacterized, unannotated small RNA and uniformly tiled across the genome with a consensus sequence of 20bp. A 3-smRC signature was significantly overexpressed in circulating EVs of HCC patients compared to controls at risk or patients with non-HCC malignancies (p<0.01, n=157). An independent validation in a phase 2 biomarker study revealed 86% sensitivity and 91% specificity for the detection of early HCC from controls at risk (i.e. cirrhosis or chronic liver disease, n=209) (positive predictive value (PPV): 89%, area under the ROC curve [AUC]: 0.87). The 3-smRC signature was independent of alpha-fetoprotein (p<0.0001) and a composite model yielded an increased AUC of 0.93 (sensitivity: 85%, specificity: 94%, PPV: 95%). ConclusionAn exRNA-based 3-smRC signature from plasma detects early stage HCC, which directly leads to the prospect of a minimally-invasive, blood-only, operator-independent surveillance biomarker. One sentence summaryWe employ a novel, data-driven approach to identify and characterize small RNA clusters from unannotated loci in extracellular vesicle-derived RNA across different cancer types, isolation techniques, and biofluids, facilitating discovery of a robust biomarker for detection of early stage liver cancer.

cancer biology↗

bioRxiv2020

Antibiotic-dependent relationships between nasal microbiome and secreted proteome in chronic rhinosinusitis and nasal polyps

BackgroundAntibiotics are commonly prescribed to treat chronic rhinosinusitis (CRS); however, the effects of antibiotics on the microbiome and secreted proteome remain unknown in regard to CRS. ObjectiveWe analyzed the effects of antibiotics on the nasal microbiome and secreted proteome in the context of CRS using multi-omic analysis. MethodsNasal secretions were collected from 29 control, 30 CRS patients without nasal polyps (CRSsNP), and 40 CRS patients with nasal polyps (CRSwNP). A total of 99 subjects were divided into two groups that included subjects who had taken antibiotics 3 months prior to sampling (ABX) and those who had not (NABX). We performed 16S rDNA sequence analyses and Orbitrap mass spectrometry-based proteomic analyses in data-independent acquisition (DIA) on the nasal secretions. Spearman correlation was used to assess the correlations between the nasal microbiome and secreted proteome. ResultsWe observed a strong association between the nasal microbiome and secreted proteome according to disease status. Antibiotic use reduced differences in the microbial community and secreted proteome according to disease status. Interestingly, in nasal polyp (NP) patients, antibiotics exhibited strong effects not only on the nasal microbiome and the secreted proteome but also on their associations. Additionally, their correlations were strengthened in subjects who had taken antibiotics. ConclusionIntegrative analyses revealed that the correlations between the microbiome and the secreted proteome could be altered and strengthened in subjects who used antibiotics. These findings provide novel insight into the effects of antibiotics on the nasal environment and the host responses in CRS.

microbiology↗

bioRxiv2019

AutoGenome: An AutoML Tool for Genomic Research

Deep learning have made great successes in traditional fields like computer vision (CV), natural language processing (NLP) and speech processing. Those achievements greatly inspire researchers in genomic study and make deep learning in genomics a very hot topic. Convolutional neural network (CNN) and recurrent neural network (RNN) are frequently used for genomic sequence prediction problems; multiple layer perception (MLP) and auto-encoders (AE) are frequently used for genomic profiling data like RNA expression data and gene mutation data. Here, we introduce a new neural network architecture, named residual fully-connected neural network (RFCN) and demonstrate its advantage for modeling genomic profiling data. We further incorporate AutoML algorithms and implement AutoGenome, an end-to-end automated genomic deep learning framework. By utilizing the proposed RFCN architectures, automatic hyper-parameter search and neural architecture search algorithms, AutoGenome can train high-performance deep learning models for various kinds of genomic profiling data automatically. To make researchers better understand the trained models, AutoGenome can assess the feature importance and export the most important features for supervised learning tasks, and the representative latent vectors for unsupervised learning tasks. We envision AutoGenome to become a popular tool in genomic studies.

genomics↗

bioRxiv2019

Intraflagellar transport complex B proteins regulate the Hippo effector Yap1 during cardiogenesis

Cilia and the intraflagellar transport (IFT) proteins involved in ciliogenesis are associated with congenital heart diseases (CHD). However, the molecular links between cilia, IFT proteins and cardiogenesis are yet to be established. Using a combination of biochemistry, genetics, and live imaging methods, we show that IFT complex B proteins (Ift88, Ift54 and Ift20) modulate the Hippo pathway effector YAP1 in zebrafish and mouse. We demonstrate that this interaction is key to restrict the formation of the proepicardium and the myocardium. In cellulo experiments suggest that IFT88 and IFT20 interact with YAP1 in the cytoplasm and functionally modulates its activity, identifying a molecular link between cilia related proteins and the Hippo pathway. Taken together, our results highlight a novel role for IFT complex B proteins during cardiogenesis and shed light on an unexpected mechanism of action for ciliary proteins in YAP1 regulation. These findings provide mechanistic insights into a non-canonical role for cilia related proteins during cardiogenesis.

developmental biology↗

bioRxiv2019

Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains

Identification of gene expression traits unique to the human brain sheds light on the mechanisms of human cognition. Here we searched for gene expression traits separating humans from other primates by analyzing 88,047 cell nuclei and 422 tissue samples representing 33 brain regions of humans, chimpanzees, bonobos, and macaques. We show that gene expression evolves rapidly within cell types, with more than two-thirds of cell type-specific differences not detected using conventional RNA sequencing of tissue samples. Neurons tend to evolve faster in all hominids, but non-neuronal cell types, such as astrocytes and oligodendrocyte progenitors, show more differences on the human lineage, including alterations of spatial distribution across neocortical layers.

evolutionary biology↗

bioRxiv2019

Single-cell genomic atlas of great ape cerebral organoids uncovers human-specific features of brain development

The human brain has changed dramatically since humans diverged from our closest living relatives, chimpanzees and the other great apes1-5. However, the genetic and developmental programs underlying this divergence are not fully understood6-8. Here, we have analyzed stem cell-derived cerebral organoids using single-cell transcriptomics (scRNA-seq) and accessible chromatin profiling (scATAC-seq) to explore gene regulatory changes that are specific to humans. We first analyze cell composition and reconstruct differentiation trajectories over the entire course of human cerebral organoid development from pluripotency, through neuroectoderm and neuroepithelial stages, followed by divergence into neuronal fates within the dorsal and ventral forebrain, midbrain and hindbrain regions. We find that brain region composition varies in organoids from different iPSC lines, yet regional gene expression patterns are largely reproducible across individuals. We then analyze chimpanzee and macaque cerebral organoids and find that human neuronal development proceeds at a delayed pace relative to the other two primates. Through pseudotemporal alignment of differentiation paths, we identify human-specific gene expression resolved to distinct cell states along progenitor to neuron lineages in the cortex. We find that chromatin accessibility is dynamic during cortex development, and identify instances of accessibility divergence between human and chimpanzee that correlate with human-specific gene expression and genetic change. Finally, we map human-specific expression in adult prefrontal cortex using single-nucleus RNA-seq and find developmental differences that persist into adulthood, as well as cell state-specific changes that occur exclusively in the adult brain. Our data provide a temporal cell atlas of great ape forebrain development, and illuminate dynamic gene regulatory features that are unique to humans.

developmental biology↗

bioRxiv2019

Lamina-specific neuronal properties promote robust, stable signal propagation in feedforward networks

Feedforward networks (FFN) are ubiquitous structures in neural systems and have been studied to understand mechanisms of reliable signal and information transmission. In many FFNs, neurons in one layer have intrinsic properties that are distinct from those in their pre-/postsynaptic layers, but how this affects network-level information processing remains unexplored. Here we show that layer-to-layer heterogeneity arising from lamina-specific cellular properties facilitates signal and information transmission in FFNs. Specifically, we found that signal transformations, made by neighboring layers of neurons on an input-driven spike signal, are complementary to each other. This mechanism boosts information transfer carried by a propagating spike signal, and thereby supports reliable spike signal and information transmission in a deep FFN. Our study suggests that distinct cell types in neural circuits have complementary computational functions and facilitate information processing on the whole.\n\nSignificance StatementNeural systems have many cell types that differ in properties such as size, shape, cellular mechanisms, etc. Furthermore, neurons often propagate signals to other neurons that have properties very different from their own. We investigated what this phenomenon implies in neural information processing by using computational network models, inspired by a recent experimental study on the olfactory neural pathway of fruit flies. We found that different types of neurons can perform complementary functions in a network, which boosts information transfer on the whole and supports robust, stable signal propagation in a \"deep\" network with many layers. Our study demonstrates that diverse cell types with different intrinsic properties are crucial for optimal signal and information transfer in neural networks.

neuroscience↗

bioRxiv2019

The Marginal Cells of the Caenorhabditis elegans Pharynx Scavenge Cholesterol and Other Hydrophobic Small Molecules

The nematode worm Caenorhabditis elegans is a bacterivore filter feeder. Through the contraction of the worms pharynx, a bacterial suspension is sucked into the pharynxs lumen. Excess liquid is then shunted out of the buccal cavity through ancillary channels that are made from specialized pharyngeal cells called marginal cells. Through the characterization of our library of worm-bioactive small molecules (a.k.a. wactives), we found that more than one third of wactives visibly accumulate inside of the marginal cells as crystals or globular spheres. Wactives that visibly accumulate are typically more hydrophobic than those that do not. To understand why wactives accumulate specifically in marginal cells, we performed a forward genetic screen for mutants that resist the lethality associated with one crystallizing wactive. We identified a presumptive sphingomyelin-synthesis pathway that is necessary for crystal and sphere accumulation. Sphingomyelin is a phospholipid that is enriched in the outer leaflet of the plasma membranes of most metazoans. We find that the predicted terminal enzyme of this pathway, sphingomyelin synthase 5 (SMS-5), is expressed in the pharynx, contributes to sphingomyelin abundance, and that its expression in marginal cells is sufficient for wactive accumulation. We also find that the expression of SMS-5 in the marginal cells is necessary for the proper absorption of exogenous cholesterol, without which C. elegans cannot develop. We conclude that the sphingomyelin-rich plasma membrane of the marginal cells acts as a sink to scavenge important hydrophobic nutrients from the filtered liquid that might otherwise be shunted back into the environment. One sentence summaryThe anterior pharynx of C. elegans is a Sink for Hydrophobic Small Molecules

developmental biology↗

bioRxiv2019

Molecular Mechanisms Driving Bistable Switch Behavior in Xylem Cell Differentiation

Plant xylem cells conduct water and mineral nutrients. Although most plant cells are totipotent, xylem cells are unusual and undergo terminal differentiation. Many genes regulating this process are well characterized, including the VASCULAR-RELATED NAC DOMAIN7 (VND7), MYB46 and MYB83 transcription factors which are proposed to act in interconnected feed-forward loops. Much less is known regarding the dynamic behavior underlying the terminal transition to xylem cell differentiation. Here we utilize whole root and single cell data to mathematically model this relationship. These provide evidence for VND7 regulating bistable switching of cells in the root to a xylem cell identity, with additional features of hysteresis. We further determine that although MYB46 responds to VND7 induction, it is not inherently involved in executing the binary switch. A novel regulatory architecture is proposed that involves four downstream targets of VND7 that act in a cycle. These data provide an important model to study the emergent properties that may give rise to totipotency relative to terminal differentiation and reveal novel xylem cell subtypes.

plant biology↗

bioRxiv2019

Nedd4 E3 ligase and beta-arrestins regulate ubiquitination, trafficking, and stability of the mGlu7 receptor

The metabotropic glutamate receptor 7 (mGlu7) is a class C G protein-coupled receptor (GPCR) that modulates excitatory neurotransmitter release at the presynaptic active zone. Although post-translational modification of cellular proteins with ubiquitin is a key molecular mechanism governing protein degradation and function, mGlu7 ubiquitination and its functional consequences have not been elucidated yet. Here, we report that Nedd4 ubiquitin E3 ligase and {beta}-arrestins regulate ubiquitination of mGlu7 in heterologous cells and neurons. Upon agonist-stimulation, {beta}-arrestins recruit Nedd4 to mGlu7 and facilitate Nedd4-mediated ubiquitination of mGlu7. Nedd4 and {beta}-arrestins regulate constitutive and agonist-induced endocytosis of mGlu7 and are required for mGlu7-dependent MAPK signaling in neurons. In addition, Nedd4-mediated ubiquitination results in the degradation of mGlu7 by both the lysosomal and proteasomal degradation pathways. These findings provide a model in which Nedd4 and {beta}-arrestin act together as a complex to regulate mGlu7 surface expression and function at the presynaptic terminals.

neuroscience↗

bioRxiv2018

A cumulative inertia phenomenon explains anomalous long-distance transport in eukaryotic cells

We demonstrate the phenomenon of cumulative inertia in intracellular transport involving multiple motor proteins in human epithelial cells by measuring the empirical survival probability of cargoes on the microtubule and their detachment rates. We found the longer a cargo moves along a microtubule, the less likely it detaches from it. As a result, the movement of cargoes is non-Markovian and involves a memory. We observe memory effects on the scale of up to 2 seconds. We provide a theoretical link between the measured detachment rate and the super-diffusive Levy walk-like cargo movement.

biophysics↗